The biggest advantage to using two channels is being able to use sub-trim to center each servo independantly. Beyond that, you can use the ability to program in differential to help the plane handle better. You can put in differential using a Y-harness as well by setting up the aileron horns slightly offset, but you can't fine-tune it like you can with a computer radio and 2 channels. That said, for most guys most of the time, it's fine.

For reference, I'm just about flight-ready with a Mosquito twin-engine plane. I have a 9 channel radio. I'm using a y-harness on ailerons, but duel elevator servos, duel throttle servos and duel flap servos all on their own channel. Because having that electronic fine-tuning is more important to me on those 3 channels than on ailerons.